outbreak! (ebola, sars, coronavirus, etc)

That Cornell thing is kind of what I was getting at about leadership basing decisions off of pure case counts. I don’t know a lot about the situation in New York State and how bad the hospitals/ICU situation is around Ithaca, and there are plenty of other factors I’m sure I know nothing about. That said, it’s surprising to see an institution with a vaccine mandate and, presumably, a very high rate of vaccination take this step. They even explain that they aren’t yet sure there actually is a lot of Omicron in what they sampled, but they are “proceeding as if it is”.

Not saying it’s the wrong decision, just seems a not great sign that we are going to see a lot of preemptive shutdowns even before we wrap our arms around Omicron.

Supposedly preliminary data suggests risk of hospitalizations is 29% less than ancestral strain, but really that calc could go either direction when we get more clinical outcomes

https://www.cnn.com/2021/12/14/health/omicron-variant-south-africa-details/index.html

One of the most salient lessons of this pandemic has been that college kids will gather and mingle in large, closely packed groups, both indoors and out, often unmasked, the instant they have the chance. They will also consume alcohol in unwise quantities, but we knew that long before the pandemic. The officials at Cornell may have taken this into account.

Well, yeah. But by that logic every campus should be shut down every single time there’s a spike, but that’s not sustainable or realistic at this point. And I’m not arguing that sometimes going remote isn’t the right decision. It’s more that seeing that news makes me think it won’t be the last and the more schools shutdown, the more employers shutdown and… well, considering we’ve killed pretty much all of the paltry, half-assed safety nets we established last year, I really worry what additional shutdowns are going to do to people in precarious financial positions. I also don’t see any of these shutdowns being approached in a measured, consistent, rational way, rather they will be half measures that don’t effectively stop the spread as much as they might otherwise and end up punishing the poor more than anything else.

I don’t know, it’s just that seeing decisions like this made in a (seeming) panic, in the middle of finals week with almost zero notice, doesn’t exactly inspire confidence that we’ve learned a lot about dealing with another huge wave. Maybe I’ll be proven wrong this time.

DePaul already announced they're coming back from break online

https://depauliaonline.com/56003/news/depaul-is-returning-to-online-classes-for-first-two-weeks-of-winter-quarter-to-combat-potential-covid-19-surge/

I know following Topol can be a mess, but I was really struck by the two graphs he’s shared this evening showing Cornell and Denmark.

The country with the highest cases/capita in the world now is Denmark, with 77% of its population fully vaccinated, 23% boosted, soon to be Omicron dominant.
(The US is 61% vaccinated, 15% boosted, avg ~120,000 cases per day, w/ >66,000 hospitalizations) pic.twitter.com/RG2MVk8tfb

— Eric Topol (@EricTopol) December 15, 2021

The O signature is a |@Cornell, graph by @AnilOza16 @cornellsun pic.twitter.com/4CNYCZcQSn

— Eric Topol (@EricTopol) December 15, 2021

I’m trying not to dwell on the doom and gloom but, this seems bad. Very bad. Even if it is 29% less severe.

One more study. More transmissible than Delta though impact is different:

For those asking whether this is good/bad news, simple answer: I don't know. While omicron may infect the lung cells less efficiently, a higher viral load may worsen immune response. We discussed the pathogenesis w/ @KindrachukJason @KrutikaKuppalli https://t.co/aAYXx8tR8a

— Muge Cevik (@mugecevik) December 15, 2021

thanks, was waiting several days for Muge to post a thorough update

the metro last night had a bit on how the main omicron symptoms that are being seen are different from the taste / fever / cough of earlier, classic covid.

(i'm wondering if it might evade not just vaccination but *testing* because of this?)

now now

I feel like Omicron evading testing means we wouldn't already have the data we do have. I'm not sure that's a worry.

Honestly what kept me up last night were the reports of areas with Omicron breakouts seeing doubling of cases every 2-3 days. That's just... crazy. Even if it is significantly milder, the sheer numbers of cases we are likely to see, coupled with the 40% of America that refuses to get vaccinated, terrifies me. If similar rates hold up here, and there is yet little argument about why it wouldn't, I don't see how our healthcare system doesn't get completely overwhelmed by mid-January. And considering very few states/municipalities have the political will for much more than indoor mask mandates, if that, I fear a surge that will dwarf all the others. The only silver lining I see is that hopefully deaths won't spike nearly as bad as cases.

yeah we're fucked

^^^ almost what I posted instead, tbh

i’m not sure this is right. yes there will be a huge wave of omicron, the question is how many people will need care. if it’s as bad as normal flu then it’s going to be pretty ugly. but it might not be. mine is like a mild cold.

You've had it already right? That would contribute to how severe it is for you this time around, per reports.

xpost - I'm glad to hear yours is mild! Hope it stays that way and I'm sorry to see it hit you again.

I am very hopeful that it does remain "mild" for the vaxxed, but the sheer numbers of unvaccinated in the US mean that there is still a fairly huge population that could get hit hard enough to overwhelm our hospitals.

yeahi dunno. i had it in march 2020.

when i say we're fucked i mean hospitals are going to be jammed for the next 6-8 months in this country and we are going to be wearing masks for the next year and i could also see some quarentining happening

right. and if you need something done that’s non-covid related well good luck with that, cause uncle steve considers it his god given right to get hospitalised with covid if he wants to

correct

the metro last night had a bit on how the main omicron symptoms that are being seen are different from the taste / fever / cough of earlier, classic covid.

(i'm wondering if it might evade not just vaccination but *testing* because of this?)

xxp koogs:

The great majority of marketed PCR kits are expected to work fine with Omicron, despite Omicron's high number of mutations concentrated in its S gene. See figure 1 in PCR performance in the SARS-CoV-2 Omicron variant of concern?. Most kits don't target the S gene at all. Only 2 of 39 kits have known issues. One oddball kit for CoV-2/Flu A/Flu B/RSV is predicted to give screwy Cts. And the TaqPath Combo kit has a known S gene target failure (SGTF) with Omicron, but as it also tests for the viruses orf1-ab and N genes, it doesn't produce many false negatives.

TaqPath's SGTF has been used as a proxy for Omicron prevalence in South Africa, the UK, Denmark and Ontario. In the UK, about half of PCR testing uses TaqPath, so only half of PCR test results may indicate the variant.

Tbh if it’s as mild as they say and people are thinking it’s a cold they’re probably not bothering to test and therefore throwing off the fatality and hospitalisation rates.

hospitalization rates, while climbing, are still well below where they were at this same point during the Delta wave in South Africa.

whether this is due to mildness of illness or actual strain being milder is still being evaluated, but it definitely means proportionately less people getting infected are receiving severe incomes.

problem is the transmissibility being as high as it is means that could still be a very high number and overwhelm health care systems.

lots of folk in my state seem to forget it is indeed a two-part equation - transmissibility+virulence/severity, not just the latter.

as Howard Forman put it, "individual" risk may be lower now, but the public health risk not so much (ie health care system).

there's also the issue in the US of how Delta is still kicking our ass so we may get a fun hybrid wave

78,610 new cases in the UK today

Deaths are still falling. Hope that trend remains that way. Hospital admissions slow or falling too.

xp calzino:

Rivalling the all time high of 81k. A UK epidemiology prof tweeted the other day that there won't be a million reported cases a day, simply because there just isn't enough testing capacity. Suspect the UK is pretty close to that threshold of every diagnostic rtPCR machine in the country running 24/7, and after that its flying half blinded.

lateral flows can be self-administered though, and reported, and presumably those add to the totals?

Guardian, yesterday: UK public hit by second day of problems obtaining Covid tests

It’d be great if Sanpaku gave it a rest tbh

Somewhat more reassuring take from Kall (who caek shared last week)

In some areas, Delta is actually rising as well which isn’t helping

For example see London, Omicron wave is ~1 week ahead of other English regions

Delta steadily increasing while Omicron is full vert 😬 https://t.co/6kMcuHwcDD

— Meaghan Kall (@kallmemeg) December 15, 2021

Ugh it didn't start at the beginning

Well if you click there the other tweets will show up

I was going to say, "THAT's the reassuring part??"

Lol

another good thread from JBM.

he and many others have noted it looks as if Gauteng may be peaking (though other SA provinces are still on the rise), which would be a really quick time for a wave to peak.

other information about the continued decoupling of hospitals/deaths from cases being observed in SA/UK and what that might mean

NEW: here’s a chart showing daily cases by specimen date in London, broken down by variant.

This is what is coming to ~every country across the world in the coming weeks. pic.twitter.com/EZsnw5evK3

— John Burn-Murdoch (@jburnmurdoch) December 15, 2021

looking at the UK (which seems to be in the process of going from a baseline of 1/1000 of the population testing positive each day to maybe up to ~1/500-1/200), we're going to stretch or possibly even exceed testing capacity in regions of the the US over the next couple of weeks. don't expect to get a same day PCR test on xmas eve.

if you can afford rapid tests, i would stock up, especially if you're planning holiday gatherings involving old people. the cheapest available to non-costco people are these https://www.amazon.com/iHealth-COVID-19-Authorized-Non-invasive-Discomfort/dp/B09KZ6TBNY/.

still not clear what the implications of all this are for hospitalizations but, well, it's not going to improve things, and i would avoid car accidents, broken bones, appendicitis etc. if at all possible.

As someone just now recovering from a broken bone who needs physical therapy but not surgery I’ll count my blessings…

(pretty reliable source, he correctly called when Florida was peaking during the worst of our Delta wave):

BREAKING: South Africa Hospitalizations
Hospitalizations ⬆️59% week over week
Gauteng Province ⬆️37%
GP⬆️2.7% from yesterday

GP approaching plateau. South Africa, overall, also slowing growth.

This wave is less impactful than Delta wave. Many deaths yet to see, however. https://t.co/Ga8ANXEdGU pic.twitter.com/GyPE7vI7A4

— (((Howard Forman))) (@thehowie) December 16, 2021

wonder to what degree vaccination mitigated the wave

the common theory is that the virus isn't actually 'less mild', but because almost everybody in Africa either got infected or vaccinated (less than 30%) against a previous strain of the virus, the protection wasn't perfect, but there was enough T-cell response/etc to keep the cases less severe than if they were a completely immune-naive population.

does bode well for countries with high levels of vaccination/natural infection, less so for those who don't have a lot of either.

still not a "nothingburger" as some suggest, as in the US alone we have 330 million people in this country and were just at over 100,000+ hospitalizations a few months ago, wrecking the system.

i'm hoping, fuckin' hoping that we avoid the worst.

confirmation from John Burn-Murdoch - cases definitely slowing and it's not an artificial artifact due to delayed reporting. Thomas Moultrie, another expert, confirms that in the comments, as someone challenges John's conclusion.

Quick situation update from Gauteng, showing all key metrics including excess deaths.

Cases and test positivity peaking, admissions slowing.

Deaths still climbing at same pace as past waves, but based on slowdown in cases we can be sure deaths will not get close to Delta peak. pic.twitter.com/Ce4xnfMOfD

— John Burn-Murdoch (@jburnmurdoch) December 16, 2021

What I think looking at that and reading about short incubation period is, it spreads fast, shows up fast and goes fast. So a short sharp wave as opposed to a long drawn out one? If so, that would make a huge difference ito the virus becoming epidemic, I think?

As someone just now recovering from a broken bone who needs physical therapy but not surgery I’ll count my blessings…
― Ned Raggett, Thursday, December 16, 2021

xp, that's what we thought about delta, and it makes sense in terms of the dynamics. and the UK delta wave dropped from it's peak very quickly in the summer. omicron could drop even quicker.

but delta cases then stabilized at a very high level for six months after that in the UK, so it's not necessarily over once it peaks.

the good(?) news is there's a real possibility this wave is so big that 1% of the UK population gets infected every day. after 30 days of that, there surely can't be enough naive hosts for the 6 months at 50,000/day the UK just had with delta.

not sure we have many hesitant parents here but ... covid isn't special. if you vaccinate your kids, vaccinate your kids against covid too.

From ACIP. We routinely vaccinate children against diseases that kill fewer than Covid before vaccines. Something nice about keeping children alive. https://t.co/yofrNn37BL pic.twitter.com/ZaJN8Lclwy

— zeynep tufekci (@zeynep) December 16, 2021

Once these antiviral treatments are approved and rolled out here next year that’s another factor, cases might remain high - though at some point that should stop being the measurable, right? - and with enough immunity from prior infection and/or vaccines, then the link between catching covid and ever needing to attend a hospital will be weaker…hopefully?

yes

antivirals have worse side effects/risks than vaccinations, and if the 30% of people who are currently unvaccinated stay that way on the assumption antivirals are like drinking a lemsip when you have a cold then that's going to go badly for them (and the health system), and obviously there's access problems (particularly in the US) with drugs that require a prescription and ongoing contact with healthcare, and pfizer currently has capacity to make 80m courses globally in 2022, which is not going to cut it.

BUT.

i don't think we'll be in the same situation next christmas, and they are part of the reason.

nyc positivity doubled in a week, wouldn't be surprised if it doubles again even faster

https://www.nbcnewyork.com/news/coronavirus/weve-never-seen-this-before-in-nyc-covid-positivity-rate-doubles-in-3-days-as-omicron-spreads/3454450/

In early November my 1 year old had a runny nose and low grade fever so the daycare made me get a PCR with a negative result before she could return. Took her the next day and waited maybe 15 minutes to get the swab. Got the result that night. On Friday a kid in her class tested positive so they shut down her room and advised us to get her tested again. My wife went up last night and they said it was a 5 hour wait. She went again at noon and they’re 81st in line. No clue if we’ll get the results tonight